X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FAnnotationFile.java;h=ae34f6b8c1b42e7d9b3b4a5fbe12bbd5ae262ec4;hb=7d6bf4ac01167499c0f4e07de63edcdd72a6d595;hp=b3a22df894f169bc408c3bef653c8eb86d691723;hpb=59c3078b53669a38f4e1c1158675691fe60349b3;p=jalview.git diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index b3a22df..ae34f6b 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@ -1,29 +1,53 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.io; -import java.io.*; -import java.net.*; -import java.util.*; - -import jalview.analysis.*; -import jalview.datamodel.*; -import jalview.schemes.*; +import jalview.analysis.Conservation; +import jalview.api.AlignViewportI; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.GraphLine; +import jalview.datamodel.HiddenSequences; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemeProperty; +import jalview.util.ColorUtils; + +import java.awt.Color; +import java.io.BufferedReader; +import java.io.FileReader; +import java.io.InputStreamReader; +import java.io.StringReader; +import java.net.URL; +import java.util.ArrayList; +import java.util.BitSet; +import java.util.Enumeration; +import java.util.Hashtable; +import java.util.List; +import java.util.Map; +import java.util.StringTokenizer; +import java.util.Vector; public class AnnotationFile { @@ -64,18 +88,18 @@ public class AnnotationFile } /** - * convenience method for pre-2.4 feature files which have no view, hidden + * convenience method for pre-2.9 annotation files which have no view, hidden * columns or hidden row keywords. * * @param annotations * @param list * @param properties - * @return feature file as a string. + * @return annotation file as a string. */ public String printAnnotations(AlignmentAnnotation[] annotations, List list, Hashtable properties) { - return printAnnotations(annotations, list, properties, null); + return printAnnotations(annotations, list, properties, null, null, null); } @@ -116,10 +140,56 @@ public class AnnotationFile * @return annotation file */ public String printAnnotations(AlignmentAnnotation[] annotations, - List list, Hashtable properties, ViewDef[] views) + List list, Hashtable properties, + ColumnSelection cs, AlignmentI al, ViewDef view) { - // TODO: resolve views issue : annotationFile could contain visible region, - // or full data + hidden region specifications for a view. + if (view != null) + { + if (view.viewname != null) + { + text.append("VIEW_DEF\t" + view.viewname + "\n"); + } + if (list == null) + { + list = view.visibleGroups; + } + if (cs == null) + { + cs = view.hiddencols; + } + if (al == null) + { + // add hidden rep sequences. + } + } + // first target - store and restore all settings for a view. + if (al != null && al.hasSeqrep()) + { + text.append("VIEW_SETREF\t" + al.getSeqrep().getName() + "\n"); + } + if (cs != null && cs.hasHiddenColumns()) + { + text.append("VIEW_HIDECOLS\t"); + List hc = cs.getHiddenColumns(); + boolean comma = false; + for (int[] r : hc) + { + if (!comma) + { + comma = true; + } + else + { + text.append(","); + } + text.append(r[0]); + text.append("-"); + text.append(r[1]); + } + text.append("\n"); + } + // TODO: allow efficient recovery of annotation data shown in several + // different views if (annotations != null) { boolean oneColour = true; @@ -131,8 +201,8 @@ public class AnnotationFile StringBuffer colours = new StringBuffer(); StringBuffer graphLine = new StringBuffer(); StringBuffer rowprops = new StringBuffer(); - Hashtable graphGroup = new Hashtable(); - Hashtable graphGroup_refs = new Hashtable(); + Hashtable graphGroup = new Hashtable(); + Hashtable graphGroup_refs = new Hashtable(); BitSet graphGroupSeen = new BitSet(); java.awt.Color color; @@ -141,16 +211,19 @@ public class AnnotationFile { row = annotations[i]; - if (!row.visible && !row.hasScore() && !(row.graphGroup>-1 && graphGroupSeen.get(row.graphGroup))) + if (!row.visible + && !row.hasScore() + && !(row.graphGroup > -1 && graphGroupSeen + .get(row.graphGroup))) { continue; } color = null; oneColour = true; - + // mark any sequence references for the row - writeSequence_Ref(refSeq ,row.sequenceRef); + writeSequence_Ref(refSeq, row.sequenceRef); refSeq = row.sequenceRef; // mark any group references for the row writeGroup_Ref(refGroup, row.groupRef); @@ -168,7 +241,7 @@ public class AnnotationFile && row.annotations[j].displayCharacter.length() > 0 && !row.annotations[j].displayCharacter .equals(" ")); hasGlyphs |= (row.annotations[j].secondaryStructure != 0 && row.annotations[j].secondaryStructure != ' '); - hasValues |= (row.annotations[j].value != Float.NaN); // NaNs can't + hasValues |= (!Float.isNaN(row.annotations[j].value)); // NaNs can't // be // rendered.. hasText |= (row.annotations[j].description != null && row.annotations[j].description @@ -217,11 +290,11 @@ public class AnnotationFile if (graphGroup.containsKey(key)) { graphGroup.put(key, graphGroup.get(key) + "\t" + row.label); - + } else { - graphGroup_refs.put(key, new Object[] { refSeq, refGroup}); + graphGroup_refs.put(key, new Object[] { refSeq, refGroup }); graphGroup.put(key, row.label); } } @@ -257,13 +330,13 @@ public class AnnotationFile } if (hasValues) { - if (row.annotations[j].value != Float.NaN) + if (!Float.isNaN(row.annotations[j].value)) { text.append(comma + row.annotations[j].value); } else { - System.err.println("Skipping NaN - not valid value."); + // System.err.println("Skipping NaN - not valid value."); text.append(comma + 0f);// row.annotations[j].value); } comma = ","; @@ -313,7 +386,9 @@ public class AnnotationFile } if (row.hasScore()) + { text.append("\t" + row.score); + } text.append(newline); @@ -338,32 +413,38 @@ public class AnnotationFile rowprops.append(row.centreColLabels); rowprops.append(newline); } + if (graphLine.length() > 0) + { + text.append(graphLine.toString()); + graphLine.setLength(0); + } } text.append(newline); text.append(colours.toString()); - text.append(graphLine.toString()); if (graphGroup.size() > 0) { SequenceI oldRefSeq = refSeq; SequenceGroup oldRefGroup = refGroup; - for (Map.Entry combine_statement:graphGroup.entrySet()) - { - Object[] seqRefAndGroup=graphGroup_refs.get(combine_statement.getKey()); - - writeSequence_Ref(refSeq, (SequenceI)seqRefAndGroup[0]); - refSeq = (SequenceI)seqRefAndGroup[0]; - - writeGroup_Ref(refGroup, (SequenceGroup)seqRefAndGroup[1]); - refGroup = (SequenceGroup)seqRefAndGroup[1]; + for (Map.Entry combine_statement : graphGroup + .entrySet()) + { + Object[] seqRefAndGroup = graphGroup_refs.get(combine_statement + .getKey()); + + writeSequence_Ref(refSeq, (SequenceI) seqRefAndGroup[0]); + refSeq = (SequenceI) seqRefAndGroup[0]; + + writeGroup_Ref(refGroup, (SequenceGroup) seqRefAndGroup[1]); + refGroup = (SequenceGroup) seqRefAndGroup[1]; text.append("COMBINE\t"); text.append(combine_statement.getValue()); text.append(newline); } writeSequence_Ref(refSeq, oldRefSeq); refSeq = oldRefSeq; - + writeGroup_Ref(refGroup, oldRefGroup); refGroup = oldRefGroup; } @@ -390,13 +471,16 @@ public class AnnotationFile text.append(properties.get(key)); } // TODO: output alignment visualization settings here if required - + // iterate through one or more views, defining, marking columns and rows + // as visible/hidden, and emmitting view properties. + // View specific annotation is } return text.toString(); } - private Object writeGroup_Ref(SequenceGroup refGroup, SequenceGroup next_refGroup) + private Object writeGroup_Ref(SequenceGroup refGroup, + SequenceGroup next_refGroup) { if (next_refGroup == null) { @@ -421,13 +505,13 @@ public class AnnotationFile return true; } } - return false; + return false; } - + private boolean writeSequence_Ref(SequenceI refSeq, SequenceI next_refSeq) { - if (next_refSeq==null) + if (next_refSeq == null) { if (refSeq != null) { @@ -498,7 +582,7 @@ public class AnnotationFile if (sg.cs != null) { text.append("colour="); - text.append(ColourSchemeProperty.getColourName(sg.cs)); + text.append(sg.cs.toString()); text.append("\t"); if (sg.cs.getThreshold() != 0) { @@ -576,26 +660,50 @@ public class AnnotationFile String refSeqId = null; + public boolean annotateAlignmentView(AlignViewportI viewport, + String file, DataSourceType protocol) + { + ColumnSelection colSel = viewport.getColumnSelection(); + if (colSel == null) + { + colSel = new ColumnSelection(); + } + boolean rslt = readAnnotationFile(viewport.getAlignment(), colSel, + file, protocol); + if (rslt && (colSel.hasSelectedColumns() || colSel.hasHiddenColumns())) + { + viewport.setColumnSelection(colSel); + } + + return rslt; + } + public boolean readAnnotationFile(AlignmentI al, String file, - String protocol) + DataSourceType sourceType) + { + return readAnnotationFile(al, null, file, sourceType); + } + + public boolean readAnnotationFile(AlignmentI al, ColumnSelection colSel, + String file, DataSourceType sourceType) { BufferedReader in = null; try { - if (protocol.equals(AppletFormatAdapter.FILE)) + if (sourceType == DataSourceType.FILE) { in = new BufferedReader(new FileReader(file)); } - else if (protocol.equals(AppletFormatAdapter.URL)) + else if (sourceType == DataSourceType.URL) { URL url = new URL(file); in = new BufferedReader(new InputStreamReader(url.openStream())); } - else if (protocol.equals(AppletFormatAdapter.PASTE)) + else if (sourceType == DataSourceType.PASTE) { in = new BufferedReader(new StringReader(file)); } - else if (protocol.equals(AppletFormatAdapter.CLASSLOADER)) + else if (sourceType == DataSourceType.CLASSLOADER) { java.io.InputStream is = getClass().getResourceAsStream("/" + file); if (is != null) @@ -605,27 +713,35 @@ public class AnnotationFile } if (in != null) { - return parseAnnotationFrom(al, in); + return parseAnnotationFrom(al, colSel, in); } } catch (Exception ex) { ex.printStackTrace(); System.out.println("Problem reading annotation file: " + ex); - if (nlinesread>0) { - System.out.println("Last read line "+nlinesread+": '"+lastread+"' (first 80 chars) ..."); + if (nlinesread > 0) + { + System.out.println("Last read line " + nlinesread + ": '" + + lastread + "' (first 80 chars) ..."); } return false; } return false; } - long nlinesread=0; - String lastread=""; - public boolean parseAnnotationFrom(AlignmentI al, BufferedReader in) - throws Exception + + long nlinesread = 0; + + String lastread = ""; + + private static String GRAPHLINE = "GRAPHLINE", COMBINE = "COMBINE"; + + public boolean parseAnnotationFrom(AlignmentI al, ColumnSelection colSel, + BufferedReader in) throws Exception { nlinesread = 0; ArrayList combineAnnotation_calls = new ArrayList(); + ArrayList deferredAnnotation_calls = new ArrayList(); boolean modified = false; String groupRef = null; Hashtable groupRefRows = new Hashtable(); @@ -670,7 +786,8 @@ public class AnnotationFile boolean jvAnnotationFile = false; while ((line = in.readLine()) != null) { - nlinesread++;lastread = new String(line); + nlinesread++; + lastread = new String(line); if (line.indexOf("#") == 0) { continue; @@ -691,7 +808,8 @@ public class AnnotationFile while ((line = in.readLine()) != null) { - nlinesread++;lastread = new String(line); + nlinesread++; + lastread = new String(line); if (line.indexOf("#") == 0 || line.indexOf("JALVIEW_ANNOTATION") > -1 || line.length() == 0) @@ -709,10 +827,11 @@ public class AnnotationFile continue; } - else if (token.equalsIgnoreCase("COMBINE")) + else if (token.equalsIgnoreCase(COMBINE)) { // keep a record of current state and resolve groupRef at end - combineAnnotation_calls.add(new Object[] { st, refSeq, groupRef}); + combineAnnotation_calls + .add(new Object[] { st, refSeq, groupRef }); modified = true; continue; } @@ -722,9 +841,11 @@ public class AnnotationFile modified = true; continue; } - else if (token.equalsIgnoreCase("GRAPHLINE")) + else if (token.equalsIgnoreCase(GRAPHLINE)) { - addLine(al, st); + // resolve at end + deferredAnnotation_calls.add(new Object[] { GRAPHLINE, st, + refSeq, groupRef }); modified = true; continue; } @@ -784,6 +905,7 @@ public class AnnotationFile else if (token.equalsIgnoreCase("SEQUENCE_GROUP")) { addGroup(al, st); + modified = true; continue; } @@ -806,6 +928,58 @@ public class AnnotationFile modified = true; continue; } + // else if (token.equalsIgnoreCase("VIEW_DEF")) + // { + // addOrSetView(al,st); + // modified = true; + // continue; + // } + else if (token.equalsIgnoreCase("VIEW_SETREF")) + { + if (refSeq != null) + { + al.setSeqrep(refSeq); + } + modified = true; + continue; + } + else if (token.equalsIgnoreCase("VIEW_HIDECOLS")) + { + if (st.hasMoreTokens()) + { + if (colSel == null) + { + colSel = new ColumnSelection(); + } + parseHideCols(colSel, st.nextToken()); + } + modified = true; + continue; + } + else if (token.equalsIgnoreCase("HIDE_INSERTIONS")) + { + SequenceI sr = refSeq == null ? al.getSeqrep() : refSeq; + if (sr == null) + { + sr = al.getSequenceAt(0); + } + if (sr != null) + { + if (colSel == null) + { + System.err + .println("Cannot process HIDE_INSERTIONS without an alignment view: Ignoring line: " + + line); + } + else + { + // consider deferring this till after the file has been parsed ? + colSel.hideInsertionsFor(sr); + } + } + modified = true; + continue; + } // Parse out the annotation row graphStyle = AlignmentAnnotation.getGraphValueFromString(token); @@ -824,7 +998,9 @@ public class AnnotationFile { description = line; if (st.hasMoreTokens()) + { line = st.nextToken(); + } } if (st.hasMoreTokens()) @@ -928,7 +1104,7 @@ public class AnnotationFile modified = true; } // Resolve the groupRefs - Hashtable groupRefLookup=new Hashtable(); + Hashtable groupRefLookup = new Hashtable(); Enumeration en = groupRefRows.keys(); while (en.hasMoreElements()) @@ -952,7 +1128,7 @@ public class AnnotationFile { matched = true; Vector rowset = (Vector) groupRefRows.get(groupRef); - groupRefLookup.put(groupRef, theGroup); + groupRefLookup.put(groupRef, theGroup); if (rowset != null && rowset.size() > 0) { AlignmentAnnotation alan = null; @@ -967,24 +1143,77 @@ public class AnnotationFile } ((Vector) groupRefRows.get(groupRef)).removeAllElements(); } + // process any deferred attribute settings for each context + for (Object[] _deferred_args : deferredAnnotation_calls) + { + if (_deferred_args[0] == GRAPHLINE) + { + addLine(al, + (StringTokenizer) _deferred_args[1], // st + (SequenceI) _deferred_args[2], // refSeq + (_deferred_args[3] == null) ? null : groupRefLookup + .get(_deferred_args[3]) // the reference + // group, or null + ); + } + } + // finally, combine all the annotation rows within each context. /** - * number of combine statements in this annotation file. Used to create new groups for combined annotation graphs without disturbing existing ones + * number of combine statements in this annotation file. Used to create + * new groups for combined annotation graphs without disturbing existing + * ones */ int combinecount = 0; - for (Object[] _combine_args:combineAnnotation_calls) { - combineAnnotations(al, + for (Object[] _combine_args : combineAnnotation_calls) + { + combineAnnotations(al, ++combinecount, (StringTokenizer) _combine_args[0], // st (SequenceI) _combine_args[1], // refSeq - (_combine_args[2]==null) ? null : groupRefLookup.get((String)_combine_args[2]) // the reference group, or null - ); + (_combine_args[2] == null) ? null : groupRefLookup + .get(_combine_args[2]) // the reference group, + // or null + ); } - } return modified; } + private void parseHideCols(ColumnSelection colSel, String nextToken) + { + StringTokenizer inval = new StringTokenizer(nextToken, ","); + while (inval.hasMoreTokens()) + { + String range = inval.nextToken().trim(); + int from, to = range.indexOf("-"); + if (to == -1) + { + from = to = Integer.parseInt(range); + if (from >= 0) + { + colSel.hideColumns(from, to); + } + } + else + { + from = Integer.parseInt(range.substring(0, to)); + if (to < range.length() - 1) + { + to = Integer.parseInt(range.substring(to + 1)); + } + else + { + to = from; + } + if (from > 0 && to >= from) + { + colSel.hideColumns(from, to); + } + } + } + } + private Object autoAnnotsKey(AlignmentAnnotation annotation, SequenceI refSeq, String groupRef) { @@ -995,29 +1224,21 @@ public class AnnotationFile Annotation parseAnnotation(String string, int graphStyle) { - boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); // don't - // do the - // glyph - // test - // if we - // don't - // want - // secondary - // structure + // don't do the glyph test if we don't want secondary structure + boolean hasSymbols = (graphStyle == AlignmentAnnotation.NO_GRAPH); String desc = null, displayChar = null; char ss = ' '; // secondaryStructure float value = 0; boolean parsedValue = false, dcset = false; // find colour here - java.awt.Color colour = null; + Color colour = null; int i = string.indexOf("["); int j = string.indexOf("]"); if (i > -1 && j > -1) { - UserColourScheme ucs = new UserColourScheme(); - - colour = ucs.getColourFromString(string.substring(i + 1, j)); + colour = ColorUtils.parseColourString(string.substring(i + 1, + j)); if (i > 0 && string.charAt(i - 1) == ',') { // clip the preceding comma as well @@ -1071,8 +1292,8 @@ public class AnnotationFile } } if (hasSymbols - && (token.equals("H") || token.equals("E") - || token.equals("S") || token.equals(" "))) + && (token.length() == 1 && "()<>[]{}AaBbCcDdEeFfGgHhIiJjKkLlMmNnOoPpQqRrSsTtUuVvWwXxYyZz" + .contains(token))) { // Either this character represents a helix or sheet // or an integer which can be displayed @@ -1119,7 +1340,7 @@ public class AnnotationFile void colourAnnotations(AlignmentI al, String label, String colour) { - UserColourScheme ucs = new UserColourScheme(colour); + Color awtColour = ColorUtils.parseColourString(colour); Annotation[] annotations; for (int i = 0; i < al.getAlignmentAnnotation().length; i++) { @@ -1130,38 +1351,42 @@ public class AnnotationFile { if (annotations[j] != null) { - annotations[j].colour = ucs.findColour('A'); + annotations[j].colour = awtColour; } } } } } - void combineAnnotations(AlignmentI al, int combineCount, StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef) + void combineAnnotations(AlignmentI al, int combineCount, + StringTokenizer st, SequenceI seqRef, SequenceGroup groupRef) { String group = st.nextToken(); // First make sure we are not overwriting the graphIndex - int graphGroup=0; + int graphGroup = 0; if (al.getAlignmentAnnotation() != null) { for (int i = 0; i < al.getAlignmentAnnotation().length; i++) { AlignmentAnnotation aa = al.getAlignmentAnnotation()[i]; - - if (aa.graphGroup>graphGroup) + + if (aa.graphGroup > graphGroup) { // try to number graphGroups in order of occurence. - graphGroup=aa.graphGroup+1; + graphGroup = aa.graphGroup + 1; } - if (aa.sequenceRef==seqRef && aa.groupRef==groupRef && aa.label.equalsIgnoreCase(group)) + if (aa.sequenceRef == seqRef && aa.groupRef == groupRef + && aa.label.equalsIgnoreCase(group)) { - if (aa.graphGroup>-1) + if (aa.graphGroup > -1) { graphGroup = aa.graphGroup; - } else { + } + else + { if (graphGroup <= combineCount) { - graphGroup=combineCount+1; + graphGroup = combineCount + 1; } aa.graphGroup = graphGroup; } @@ -1176,7 +1401,8 @@ public class AnnotationFile for (int i = 0; i < al.getAlignmentAnnotation().length; i++) { AlignmentAnnotation aa = al.getAlignmentAnnotation()[i]; - if (aa.sequenceRef==seqRef && aa.groupRef==groupRef && aa.label.equalsIgnoreCase(group)) + if (aa.sequenceRef == seqRef && aa.groupRef == groupRef + && aa.label.equalsIgnoreCase(group)) { aa.graphGroup = graphGroup; break; @@ -1191,36 +1417,39 @@ public class AnnotationFile } } - void addLine(AlignmentI al, StringTokenizer st) + void addLine(AlignmentI al, StringTokenizer st, SequenceI seqRef, + SequenceGroup groupRef) { String group = st.nextToken(); - AlignmentAnnotation annotation = null, alannot[] = al - .getAlignmentAnnotation(); + AlignmentAnnotation[] alannot = al.getAlignmentAnnotation(); + String nextToken = st.nextToken(); + float value = 0f; + try + { + value = Float.valueOf(nextToken); + } catch (NumberFormatException e) + { + System.err.println("line " + nlinesread + ": Threshold '" + nextToken + + "' invalid, setting to zero"); + } + String label = st.hasMoreTokens() ? st.nextToken() : null; + Color colour = null; + if (st.hasMoreTokens()) + { + colour = ColorUtils.parseColourString(st.nextToken()); + } if (alannot != null) { for (int i = 0; i < alannot.length; i++) { - if (alannot[i].label.equalsIgnoreCase(group)) + if (alannot[i].label.equalsIgnoreCase(group) + && (seqRef == null || alannot[i].sequenceRef == seqRef) + && (groupRef == null || alannot[i].groupRef == groupRef)) { - annotation = alannot[i]; - break; + alannot[i].setThreshold(new GraphLine(value, label, colour)); } } } - if (annotation == null) - { - return; - } - float value = new Float(st.nextToken()).floatValue(); - String label = st.hasMoreTokens() ? st.nextToken() : null; - java.awt.Color colour = null; - if (st.hasMoreTokens()) - { - UserColourScheme ucs = new UserColourScheme(st.nextToken()); - colour = ucs.findColour('A'); - } - - annotation.setThreshold(new GraphLine(value, label, colour)); } void addGroup(AlignmentI al, StringTokenizer st) @@ -1394,7 +1623,7 @@ public class AnnotationFile } else if (key.equalsIgnoreCase("colour")) { - sg.cs = ColourSchemeProperty.getColour(al, value); + sg.cs = ColourSchemeProperty.getColourScheme(al, value); } else if (key.equalsIgnoreCase("pidThreshold")) { @@ -1404,8 +1633,7 @@ public class AnnotationFile else if (key.equalsIgnoreCase("consThreshold")) { sg.cs.setConservationInc(Integer.parseInt(value)); - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.getSequences(null), + Conservation c = new Conservation("Group", sg.getSequences(null), sg.getStartRes(), sg.getEndRes() + 1); c.calculate(); @@ -1416,7 +1644,7 @@ public class AnnotationFile } else if (key.equalsIgnoreCase("outlineColour")) { - sg.setOutlineColour(new UserColourScheme(value).findColour('A')); + sg.setOutlineColour(ColorUtils.parseColourString(value)); } else if (key.equalsIgnoreCase("displayBoxes")) { @@ -1436,11 +1664,11 @@ public class AnnotationFile } else if (key.equalsIgnoreCase("textCol1")) { - sg.textColour = new UserColourScheme(value).findColour('A'); + sg.textColour = ColorUtils.parseColourString(value); } else if (key.equalsIgnoreCase("textCol2")) { - sg.textColour2 = new UserColourScheme(value).findColour('A'); + sg.textColour2 = ColorUtils.parseColourString(value); } else if (key.equalsIgnoreCase("textColThreshold")) { @@ -1448,9 +1676,8 @@ public class AnnotationFile } else if (key.equalsIgnoreCase("idColour")) { - // consider warning if colour doesn't resolve to a real colour - sg.setIdColour((def = new UserColourScheme(value)) - .findColour('A')); + Color idColour = ColorUtils.parseColourString(value); + sg.setIdColour(idColour == null ? Color.black : idColour); } else if (key.equalsIgnoreCase("hide")) { @@ -1526,6 +1753,10 @@ public class AnnotationFile */ public String printCSVAnnotations(AlignmentAnnotation[] annotations) { + if (annotations == null) + { + return ""; + } StringBuffer sp = new StringBuffer(); for (int i = 0; i < annotations.length; i++) { @@ -1550,4 +1781,19 @@ public class AnnotationFile } return sp.toString(); } + + public String printAnnotationsForView(AlignViewportI viewport) + { + return printAnnotations(viewport.isShowAnnotation() ? viewport + .getAlignment().getAlignmentAnnotation() : null, viewport + .getAlignment().getGroups(), viewport.getAlignment() + .getProperties(), viewport.getColumnSelection(), + viewport.getAlignment(), null); + } + + public String printAnnotationsForAlignment(AlignmentI al) + { + return printAnnotations(al.getAlignmentAnnotation(), al.getGroups(), + al.getProperties(), null, al, null); + } }